Multiple sequence alignment - TraesCS5B01G547500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G547500 chr5B 100.000 2510 0 0 1 2510 700418859 700416350 0.000000e+00 4636.0
1 TraesCS5B01G547500 chr5B 89.888 89 5 2 1699 1784 700390511 700390424 7.340000e-21 111.0
2 TraesCS5B01G547500 chr5D 91.877 1822 84 18 737 2510 548954260 548952455 0.000000e+00 2486.0
3 TraesCS5B01G547500 chr5D 93.692 428 22 4 1 427 266083931 266084354 9.790000e-179 636.0
4 TraesCS5B01G547500 chr5D 93.662 284 17 1 424 707 266084308 266084590 8.300000e-115 424.0
5 TraesCS5B01G547500 chr5D 91.827 208 11 2 2226 2432 548954814 548954612 4.090000e-73 285.0
6 TraesCS5B01G547500 chr4A 91.884 1454 63 14 860 2272 620290472 620289033 0.000000e+00 1980.0
7 TraesCS5B01G547500 chr4A 92.541 429 26 4 1 427 580695100 580695524 5.940000e-171 610.0
8 TraesCS5B01G547500 chr4A 92.776 263 14 3 424 682 580695477 580695738 2.360000e-100 375.0
9 TraesCS5B01G547500 chr4A 90.751 173 12 2 737 909 620290471 620290639 6.980000e-56 228.0
10 TraesCS5B01G547500 chr6A 96.956 427 12 1 1 427 85219613 85220038 0.000000e+00 715.0
11 TraesCS5B01G547500 chr6A 94.406 286 13 2 424 707 85219992 85220276 1.070000e-118 436.0
12 TraesCS5B01G547500 chr6A 73.177 809 163 39 856 1636 608285442 608284660 2.490000e-60 243.0
13 TraesCS5B01G547500 chr2D 96.420 419 15 0 9 427 516653941 516654359 0.000000e+00 691.0
14 TraesCS5B01G547500 chr2D 94.366 284 14 1 424 707 516654313 516654594 3.830000e-118 435.0
15 TraesCS5B01G547500 chr1A 93.750 432 21 5 1 432 20403958 20404383 0.000000e+00 643.0
16 TraesCS5B01G547500 chr1A 91.809 293 15 5 424 711 20404335 20404623 1.400000e-107 399.0
17 TraesCS5B01G547500 chr6B 93.911 427 18 4 1 427 112885609 112885191 2.720000e-179 638.0
18 TraesCS5B01G547500 chr6B 93.640 283 16 1 427 707 112885234 112884952 2.990000e-114 422.0
19 TraesCS5B01G547500 chr6B 75.193 649 123 28 856 1488 703389566 703388940 3.180000e-69 272.0
20 TraesCS5B01G547500 chr3D 93.443 427 24 3 1 427 91212063 91211641 4.560000e-177 630.0
21 TraesCS5B01G547500 chr3D 94.306 281 14 2 427 707 91211683 91211405 1.780000e-116 429.0
22 TraesCS5B01G547500 chr4D 93.007 429 24 4 1 427 63779933 63779509 2.740000e-174 621.0
23 TraesCS5B01G547500 chr4D 93.262 282 17 2 427 707 63779553 63779273 5.000000e-112 414.0
24 TraesCS5B01G547500 chr2B 92.056 428 28 4 1 427 225530974 225530552 4.620000e-167 597.0
25 TraesCS5B01G547500 chr2B 91.864 295 16 4 417 707 225530607 225530317 3.010000e-109 405.0
26 TraesCS5B01G547500 chr2B 90.244 41 4 0 2393 2433 654751029 654751069 1.000000e-03 54.7
27 TraesCS5B01G547500 chr6D 74.579 653 123 30 856 1488 461501495 461500866 1.930000e-61 246.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G547500 chr5B 700416350 700418859 2509 True 4636.0 4636 100.0000 1 2510 1 chr5B.!!$R2 2509
1 TraesCS5B01G547500 chr5D 548952455 548954814 2359 True 1385.5 2486 91.8520 737 2510 2 chr5D.!!$R1 1773
2 TraesCS5B01G547500 chr5D 266083931 266084590 659 False 530.0 636 93.6770 1 707 2 chr5D.!!$F1 706
3 TraesCS5B01G547500 chr4A 620289033 620290472 1439 True 1980.0 1980 91.8840 860 2272 1 chr4A.!!$R1 1412
4 TraesCS5B01G547500 chr4A 580695100 580695738 638 False 492.5 610 92.6585 1 682 2 chr4A.!!$F2 681
5 TraesCS5B01G547500 chr6A 85219613 85220276 663 False 575.5 715 95.6810 1 707 2 chr6A.!!$F1 706
6 TraesCS5B01G547500 chr6A 608284660 608285442 782 True 243.0 243 73.1770 856 1636 1 chr6A.!!$R1 780
7 TraesCS5B01G547500 chr2D 516653941 516654594 653 False 563.0 691 95.3930 9 707 2 chr2D.!!$F1 698
8 TraesCS5B01G547500 chr1A 20403958 20404623 665 False 521.0 643 92.7795 1 711 2 chr1A.!!$F1 710
9 TraesCS5B01G547500 chr6B 112884952 112885609 657 True 530.0 638 93.7755 1 707 2 chr6B.!!$R2 706
10 TraesCS5B01G547500 chr6B 703388940 703389566 626 True 272.0 272 75.1930 856 1488 1 chr6B.!!$R1 632
11 TraesCS5B01G547500 chr3D 91211405 91212063 658 True 529.5 630 93.8745 1 707 2 chr3D.!!$R1 706
12 TraesCS5B01G547500 chr4D 63779273 63779933 660 True 517.5 621 93.1345 1 707 2 chr4D.!!$R1 706
13 TraesCS5B01G547500 chr2B 225530317 225530974 657 True 501.0 597 91.9600 1 707 2 chr2B.!!$R1 706
14 TraesCS5B01G547500 chr6D 461500866 461501495 629 True 246.0 246 74.5790 856 1488 1 chr6D.!!$R1 632

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
851 881 0.521735 CGTGGTTTAAAGAGCCAGCC 59.478 55.0 0.0 0.0 39.54 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2269 0.684153 AATGCCCATCCTTCCCAACG 60.684 55.0 0.0 0.0 0.0 4.1 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 163 8.154856 TCTTCTAAAACATACTGTTGCCTACTT 58.845 33.333 0.00 0.00 40.14 2.24
260 263 2.649531 TGGACCGTCCTCATTTGTTT 57.350 45.000 18.54 0.00 37.46 2.83
403 410 7.342541 TCATCCATTCTGATTTTGAGGCAAATA 59.657 33.333 0.00 0.00 33.19 1.40
404 411 7.664552 TCCATTCTGATTTTGAGGCAAATAT 57.335 32.000 0.00 0.00 33.19 1.28
405 412 8.765488 TCCATTCTGATTTTGAGGCAAATATA 57.235 30.769 0.00 0.00 33.19 0.86
407 414 9.635520 CCATTCTGATTTTGAGGCAAATATATC 57.364 33.333 0.00 0.00 33.19 1.63
411 418 9.412460 TCTGATTTTGAGGCAAATATATCAAGT 57.588 29.630 0.00 0.00 31.87 3.16
442 449 9.823647 TTTTTGTTCTATTCTAATTTTGTGGCA 57.176 25.926 0.00 0.00 0.00 4.92
443 450 9.823647 TTTTGTTCTATTCTAATTTTGTGGCAA 57.176 25.926 0.00 0.00 0.00 4.52
444 451 9.823647 TTTGTTCTATTCTAATTTTGTGGCAAA 57.176 25.926 0.00 0.00 0.00 3.68
697 714 2.983030 GTGGCATCACACGGGCAA 60.983 61.111 0.00 0.00 43.13 4.52
708 725 4.018490 TCACACGGGCAATCTACTAGTAA 58.982 43.478 3.76 0.00 0.00 2.24
709 726 4.647853 TCACACGGGCAATCTACTAGTAAT 59.352 41.667 3.76 0.00 0.00 1.89
710 727 5.829391 TCACACGGGCAATCTACTAGTAATA 59.171 40.000 3.76 0.00 0.00 0.98
711 728 6.016527 TCACACGGGCAATCTACTAGTAATAG 60.017 42.308 3.76 0.00 0.00 1.73
712 729 6.016527 CACACGGGCAATCTACTAGTAATAGA 60.017 42.308 3.83 0.00 33.27 1.98
713 730 6.016443 ACACGGGCAATCTACTAGTAATAGAC 60.016 42.308 3.83 0.00 31.54 2.59
714 731 6.016527 CACGGGCAATCTACTAGTAATAGACA 60.017 42.308 3.83 0.00 31.54 3.41
715 732 6.207025 ACGGGCAATCTACTAGTAATAGACAG 59.793 42.308 3.83 1.18 31.54 3.51
716 733 6.349445 CGGGCAATCTACTAGTAATAGACAGG 60.349 46.154 3.83 0.00 31.54 4.00
717 734 6.494146 GGGCAATCTACTAGTAATAGACAGGT 59.506 42.308 3.83 0.00 31.54 4.00
718 735 7.015389 GGGCAATCTACTAGTAATAGACAGGTT 59.985 40.741 3.83 0.81 31.54 3.50
719 736 7.868415 GGCAATCTACTAGTAATAGACAGGTTG 59.132 40.741 17.50 17.50 31.54 3.77
720 737 7.868415 GCAATCTACTAGTAATAGACAGGTTGG 59.132 40.741 20.53 10.24 31.54 3.77
721 738 6.956202 TCTACTAGTAATAGACAGGTTGGC 57.044 41.667 3.83 0.00 0.00 4.52
722 739 6.670617 TCTACTAGTAATAGACAGGTTGGCT 58.329 40.000 3.83 0.00 40.22 4.75
723 740 7.809238 TCTACTAGTAATAGACAGGTTGGCTA 58.191 38.462 3.83 0.00 43.12 3.93
724 741 6.712179 ACTAGTAATAGACAGGTTGGCTAC 57.288 41.667 3.83 0.00 41.49 3.58
725 742 6.192773 ACTAGTAATAGACAGGTTGGCTACA 58.807 40.000 3.83 0.00 41.49 2.74
726 743 5.599999 AGTAATAGACAGGTTGGCTACAG 57.400 43.478 0.80 0.00 41.49 2.74
727 744 5.024118 AGTAATAGACAGGTTGGCTACAGT 58.976 41.667 0.80 0.00 41.49 3.55
728 745 6.192773 AGTAATAGACAGGTTGGCTACAGTA 58.807 40.000 0.80 0.00 41.49 2.74
729 746 6.839657 AGTAATAGACAGGTTGGCTACAGTAT 59.160 38.462 0.80 0.00 41.49 2.12
730 747 3.895232 AGACAGGTTGGCTACAGTATG 57.105 47.619 0.80 0.00 30.85 2.39
749 766 4.999469 ATGTACATATCAGGGCCATCAA 57.001 40.909 6.56 0.00 0.00 2.57
769 786 7.281324 CCATCAATGCATGTTGATTAACCAAAT 59.719 33.333 11.92 0.00 44.23 2.32
794 824 9.706691 ATATACGAGTATTTGTGTTCATAAGGG 57.293 33.333 0.73 0.00 0.00 3.95
804 834 9.737844 ATTTGTGTTCATAAGGGCAATATTTTT 57.262 25.926 0.00 0.00 0.00 1.94
838 868 4.782019 ATGTTCATAAATGCACGTGGTT 57.218 36.364 18.88 0.00 0.00 3.67
851 881 0.521735 CGTGGTTTAAAGAGCCAGCC 59.478 55.000 0.00 0.00 39.54 4.85
852 882 1.616159 GTGGTTTAAAGAGCCAGCCA 58.384 50.000 0.00 0.00 39.54 4.75
924 957 2.089887 TTAGTGCTCGGTTCGGTGCA 62.090 55.000 3.70 3.70 35.46 4.57
938 971 5.123344 GGTTCGGTGCATAAATTAGACTTGT 59.877 40.000 0.00 0.00 0.00 3.16
969 1010 2.164219 TGATCAATCCTCGCAAAAAGCC 59.836 45.455 0.00 0.00 41.38 4.35
995 1036 7.208225 TGTATGCTGTACTTGCAAACAAATA 57.792 32.000 15.68 2.02 44.01 1.40
1183 1228 4.157120 ATACGCGTGGACTGGCCC 62.157 66.667 24.59 0.00 34.97 5.80
1413 1458 1.999648 TTGCATTGTTTGAGGGAGCT 58.000 45.000 0.00 0.00 0.00 4.09
1414 1459 1.538047 TGCATTGTTTGAGGGAGCTC 58.462 50.000 4.71 4.71 0.00 4.09
1426 1471 0.105778 GGGAGCTCAGAAGAATCCCG 59.894 60.000 17.19 0.00 39.15 5.14
1443 1488 0.734253 CCGTGCAGGAAGAGAACTCG 60.734 60.000 8.24 0.00 45.00 4.18
1574 1635 3.041946 GAGATGTCTCCACCCCTTACAT 58.958 50.000 0.00 0.00 37.02 2.29
1575 1636 2.774234 AGATGTCTCCACCCCTTACATG 59.226 50.000 0.00 0.00 31.19 3.21
1576 1637 2.038863 TGTCTCCACCCCTTACATGT 57.961 50.000 2.69 2.69 0.00 3.21
1577 1638 1.906574 TGTCTCCACCCCTTACATGTC 59.093 52.381 0.00 0.00 0.00 3.06
1578 1639 1.134788 GTCTCCACCCCTTACATGTCG 60.135 57.143 0.00 0.00 0.00 4.35
1579 1640 0.902531 CTCCACCCCTTACATGTCGT 59.097 55.000 0.00 0.00 0.00 4.34
1580 1641 0.611200 TCCACCCCTTACATGTCGTG 59.389 55.000 0.00 2.42 0.00 4.35
1621 1682 6.697019 TCTCTTTTGCTTGTTTAAACATGAGC 59.303 34.615 27.14 27.14 41.09 4.26
1637 1698 2.241160 TGAGCCATCTGCAATGTGTTT 58.759 42.857 7.71 0.00 44.83 2.83
1664 1750 5.447624 ACTGTTTGTTTAGCACCCATAAC 57.552 39.130 0.00 0.00 0.00 1.89
1684 1770 2.567615 ACCAGATCTCAACTGTGGTACC 59.432 50.000 4.43 4.43 39.80 3.34
1690 1776 7.038729 CCAGATCTCAACTGTGGTACCATATAT 60.039 40.741 19.72 3.68 34.04 0.86
1721 1807 8.798859 AGATTCATTAGCAGTGAACAGTTTAT 57.201 30.769 0.00 0.00 38.31 1.40
1722 1808 9.890629 AGATTCATTAGCAGTGAACAGTTTATA 57.109 29.630 0.00 0.00 38.31 0.98
1791 1877 7.923414 ATACAAATTCACTGGGTTCTAGTTC 57.077 36.000 0.00 0.00 0.00 3.01
1885 1971 6.122277 TGAGAACCAGATCTTCAAACACTTT 58.878 36.000 0.00 0.00 0.00 2.66
1955 2041 2.822707 AGTAGGATAGTGTGTCGGGT 57.177 50.000 0.00 0.00 0.00 5.28
2073 2160 1.137675 CAATCTGTCTGCGAGGATGGA 59.862 52.381 0.00 0.00 0.00 3.41
2155 2244 1.668751 GATTTCATTACGGGCTTCGCA 59.331 47.619 0.29 0.00 43.89 5.10
2179 2269 1.845809 CGGCTTCCAGTGCTGTTGTC 61.846 60.000 0.00 0.00 32.57 3.18
2181 2271 1.160329 GCTTCCAGTGCTGTTGTCGT 61.160 55.000 0.00 0.00 0.00 4.34
2186 2276 0.813610 CAGTGCTGTTGTCGTTGGGA 60.814 55.000 0.00 0.00 0.00 4.37
2205 2299 3.219198 GGATGGGCATTGCGGACC 61.219 66.667 1.91 0.00 0.00 4.46
2280 2374 9.461312 AAGATAACACAAGTATTTGGAATAGCA 57.539 29.630 2.81 0.00 38.66 3.49
2281 2375 9.461312 AGATAACACAAGTATTTGGAATAGCAA 57.539 29.630 2.81 0.00 38.66 3.91
2282 2376 9.503427 GATAACACAAGTATTTGGAATAGCAAC 57.497 33.333 2.81 0.00 38.66 4.17
2283 2377 7.524717 AACACAAGTATTTGGAATAGCAACT 57.475 32.000 2.81 0.00 38.66 3.16
2284 2378 6.913170 ACACAAGTATTTGGAATAGCAACTG 58.087 36.000 2.81 0.00 38.66 3.16
2294 2388 4.756642 TGGAATAGCAACTGAACTGAACTG 59.243 41.667 0.00 0.00 0.00 3.16
2310 2404 3.056107 TGAACTGAACTGTAATCCCTCCG 60.056 47.826 0.00 0.00 0.00 4.63
2329 2423 6.418956 CCTCCGTTTCATAATTATTGTCACG 58.581 40.000 0.00 2.81 0.00 4.35
2349 2443 9.190858 TGTCACGGATTTATTTGAAATTTGAAG 57.809 29.630 0.00 0.00 0.00 3.02
2403 2497 3.978610 AGTAGTACTTCCTTCGTCCCAT 58.021 45.455 0.00 0.00 0.00 4.00
2426 2520 8.916654 CCATAATAAGTGTCGCTGATTTAGTAG 58.083 37.037 1.17 0.00 30.92 2.57
2438 2532 7.866393 TCGCTGATTTAGTAGAAAGTTATAGGC 59.134 37.037 0.00 0.00 0.00 3.93
2471 2565 4.568072 ACTTAGGTTACACATGGCATCA 57.432 40.909 0.00 0.00 0.00 3.07
2501 2595 2.023673 GCTATTGGCTATTGCACACCA 58.976 47.619 9.98 0.00 41.91 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
282 285 3.243336 CGTAGGACTGCAGAAGTGTTAC 58.757 50.000 23.35 11.98 40.07 2.50
416 423 9.823647 TGCCACAAAATTAGAATAGAACAAAAA 57.176 25.926 0.00 0.00 0.00 1.94
417 424 9.823647 TTGCCACAAAATTAGAATAGAACAAAA 57.176 25.926 0.00 0.00 0.00 2.44
418 425 9.823647 TTTGCCACAAAATTAGAATAGAACAAA 57.176 25.926 0.00 0.00 0.00 2.83
560 573 8.893563 ATAAGATAACATCCCCTCAAACAAAA 57.106 30.769 0.00 0.00 0.00 2.44
686 703 2.453521 ACTAGTAGATTGCCCGTGTGA 58.546 47.619 3.59 0.00 0.00 3.58
688 705 6.016443 GTCTATTACTAGTAGATTGCCCGTGT 60.016 42.308 3.59 0.00 31.41 4.49
697 714 7.299134 AGCCAACCTGTCTATTACTAGTAGAT 58.701 38.462 3.59 3.29 31.41 1.98
708 725 4.962995 ACATACTGTAGCCAACCTGTCTAT 59.037 41.667 0.00 0.00 0.00 1.98
709 726 4.350245 ACATACTGTAGCCAACCTGTCTA 58.650 43.478 0.00 0.00 0.00 2.59
710 727 3.173965 ACATACTGTAGCCAACCTGTCT 58.826 45.455 0.00 0.00 0.00 3.41
711 728 3.611766 ACATACTGTAGCCAACCTGTC 57.388 47.619 0.00 0.00 0.00 3.51
712 729 3.835978 TGTACATACTGTAGCCAACCTGT 59.164 43.478 0.00 0.00 32.84 4.00
713 730 4.465632 TGTACATACTGTAGCCAACCTG 57.534 45.455 0.00 0.00 32.84 4.00
714 731 6.553476 TGATATGTACATACTGTAGCCAACCT 59.447 38.462 17.69 0.00 32.84 3.50
715 732 6.755206 TGATATGTACATACTGTAGCCAACC 58.245 40.000 17.69 0.00 32.84 3.77
716 733 6.868864 CCTGATATGTACATACTGTAGCCAAC 59.131 42.308 17.69 0.00 32.84 3.77
717 734 6.014584 CCCTGATATGTACATACTGTAGCCAA 60.015 42.308 17.69 0.00 32.84 4.52
718 735 5.480422 CCCTGATATGTACATACTGTAGCCA 59.520 44.000 17.69 6.77 32.84 4.75
719 736 5.624738 GCCCTGATATGTACATACTGTAGCC 60.625 48.000 17.69 1.37 32.84 3.93
720 737 5.411781 GCCCTGATATGTACATACTGTAGC 58.588 45.833 17.69 13.82 32.84 3.58
721 738 5.480422 TGGCCCTGATATGTACATACTGTAG 59.520 44.000 17.69 12.42 32.84 2.74
722 739 5.399113 TGGCCCTGATATGTACATACTGTA 58.601 41.667 17.69 0.00 0.00 2.74
723 740 4.231273 TGGCCCTGATATGTACATACTGT 58.769 43.478 17.69 2.36 0.00 3.55
724 741 4.890158 TGGCCCTGATATGTACATACTG 57.110 45.455 17.69 13.92 0.00 2.74
725 742 5.093677 TGATGGCCCTGATATGTACATACT 58.906 41.667 17.69 7.50 0.00 2.12
726 743 5.420725 TGATGGCCCTGATATGTACATAC 57.579 43.478 17.69 11.91 0.00 2.39
727 744 6.417258 CATTGATGGCCCTGATATGTACATA 58.583 40.000 17.65 17.65 0.00 2.29
728 745 4.999469 TTGATGGCCCTGATATGTACAT 57.001 40.909 13.93 13.93 0.00 2.29
729 746 4.654915 CATTGATGGCCCTGATATGTACA 58.345 43.478 0.00 0.00 0.00 2.90
730 747 3.441572 GCATTGATGGCCCTGATATGTAC 59.558 47.826 0.00 0.00 0.00 2.90
731 748 3.074242 TGCATTGATGGCCCTGATATGTA 59.926 43.478 0.00 0.00 0.00 2.29
732 749 2.158430 TGCATTGATGGCCCTGATATGT 60.158 45.455 0.00 0.00 0.00 2.29
733 750 2.521126 TGCATTGATGGCCCTGATATG 58.479 47.619 0.00 0.00 0.00 1.78
734 751 2.984435 TGCATTGATGGCCCTGATAT 57.016 45.000 0.00 0.00 0.00 1.63
735 752 2.158430 ACATGCATTGATGGCCCTGATA 60.158 45.455 0.00 0.00 0.00 2.15
736 753 1.338107 CATGCATTGATGGCCCTGAT 58.662 50.000 0.00 0.00 0.00 2.90
737 754 0.032912 ACATGCATTGATGGCCCTGA 60.033 50.000 0.00 0.00 0.00 3.86
738 755 0.828022 AACATGCATTGATGGCCCTG 59.172 50.000 0.00 0.00 0.00 4.45
739 756 0.828022 CAACATGCATTGATGGCCCT 59.172 50.000 0.00 0.00 0.00 5.19
740 757 0.825410 TCAACATGCATTGATGGCCC 59.175 50.000 0.00 0.00 33.62 5.80
749 766 8.845227 TCGTATATTTGGTTAATCAACATGCAT 58.155 29.630 0.00 0.00 36.29 3.96
769 786 7.654520 GCCCTTATGAACACAAATACTCGTATA 59.345 37.037 0.00 0.00 0.00 1.47
807 837 9.890085 CGTGCATTTATGAACATAAATTTCAAG 57.110 29.630 22.23 19.81 46.26 3.02
809 839 8.858186 CACGTGCATTTATGAACATAAATTTCA 58.142 29.630 22.23 19.71 46.26 2.69
810 840 8.320295 CCACGTGCATTTATGAACATAAATTTC 58.680 33.333 22.23 18.16 46.26 2.17
811 841 7.816995 ACCACGTGCATTTATGAACATAAATTT 59.183 29.630 22.23 8.20 46.26 1.82
814 844 6.260870 ACCACGTGCATTTATGAACATAAA 57.739 33.333 18.12 18.12 44.47 1.40
831 861 1.235724 GCTGGCTCTTTAAACCACGT 58.764 50.000 0.00 0.00 0.00 4.49
838 868 0.620556 CTCCCTGGCTGGCTCTTTAA 59.379 55.000 4.64 0.00 0.00 1.52
924 957 8.531982 TCACTGCACTCTACAAGTCTAATTTAT 58.468 33.333 0.00 0.00 35.45 1.40
938 971 3.067320 CGAGGATTGATCACTGCACTCTA 59.933 47.826 7.31 0.00 0.00 2.43
969 1010 5.107109 TGTTTGCAAGTACAGCATACAAG 57.893 39.130 23.67 0.00 46.01 3.16
995 1036 2.289694 ACGGTAAGAGTCTGCATTTGCT 60.290 45.455 3.94 0.00 42.66 3.91
1161 1206 1.666311 GCCAGTCCACGCGTATCTATC 60.666 57.143 13.44 0.00 0.00 2.08
1183 1228 3.950794 TTAGGTTGGCGGCAGCGAG 62.951 63.158 19.11 0.00 46.35 5.03
1188 1233 3.943691 ACGGTTAGGTTGGCGGCA 61.944 61.111 7.97 7.97 0.00 5.69
1413 1458 0.250234 CCTGCACGGGATTCTTCTGA 59.750 55.000 0.00 0.00 0.00 3.27
1414 1459 0.250234 TCCTGCACGGGATTCTTCTG 59.750 55.000 0.00 0.00 0.00 3.02
1426 1471 0.603569 TCCGAGTTCTCTTCCTGCAC 59.396 55.000 0.00 0.00 0.00 4.57
1443 1488 1.672737 CGGGCCAAAGCTTGATTTTCC 60.673 52.381 4.39 0.00 39.73 3.13
1574 1635 2.414179 GGGACACGACACACGACA 59.586 61.111 0.00 0.00 45.77 4.35
1575 1636 2.355481 GGGGACACGACACACGAC 60.355 66.667 0.00 0.00 45.77 4.34
1576 1637 3.608662 GGGGGACACGACACACGA 61.609 66.667 0.00 0.00 45.77 4.35
1578 1639 0.883370 GAAAGGGGGACACGACACAC 60.883 60.000 0.00 0.00 0.00 3.82
1579 1640 1.052124 AGAAAGGGGGACACGACACA 61.052 55.000 0.00 0.00 0.00 3.72
1580 1641 0.320508 GAGAAAGGGGGACACGACAC 60.321 60.000 0.00 0.00 0.00 3.67
1637 1698 2.882137 GGTGCTAAACAAACAGTAGGCA 59.118 45.455 0.00 0.00 0.00 4.75
1664 1750 2.567169 TGGTACCACAGTTGAGATCTGG 59.433 50.000 11.60 0.00 37.25 3.86
1690 1776 9.702494 CTGTTCACTGCTAATGAATCTATGATA 57.298 33.333 2.01 0.00 38.31 2.15
1696 1782 8.798859 ATAAACTGTTCACTGCTAATGAATCT 57.201 30.769 0.00 0.00 38.31 2.40
1721 1807 5.875224 TCATCATGTTTTGGAGGACAAGTA 58.125 37.500 0.00 0.00 40.82 2.24
1722 1808 4.728772 TCATCATGTTTTGGAGGACAAGT 58.271 39.130 0.00 0.00 40.82 3.16
1791 1877 7.148407 GGTTGTGAATTGTGAGGATAGTACAAG 60.148 40.741 0.00 0.00 37.69 3.16
1885 1971 5.635417 TCGTATCCAATCAATGCAAACAA 57.365 34.783 0.00 0.00 0.00 2.83
1972 2058 4.806247 CGTCAAGCTCTAGGAAACATAAGG 59.194 45.833 0.00 0.00 0.00 2.69
2113 2200 0.896226 GGGAAACTAGTGACGAGCCT 59.104 55.000 0.00 0.00 0.00 4.58
2179 2269 0.684153 AATGCCCATCCTTCCCAACG 60.684 55.000 0.00 0.00 0.00 4.10
2181 2271 0.977108 GCAATGCCCATCCTTCCCAA 60.977 55.000 0.00 0.00 0.00 4.12
2186 2276 1.754234 GTCCGCAATGCCCATCCTT 60.754 57.895 0.00 0.00 0.00 3.36
2205 2299 1.421485 GCGAACGAGTGATGGCTTG 59.579 57.895 0.00 0.00 0.00 4.01
2280 2374 6.483640 GGATTACAGTTCAGTTCAGTTCAGTT 59.516 38.462 0.00 0.00 0.00 3.16
2281 2375 5.992217 GGATTACAGTTCAGTTCAGTTCAGT 59.008 40.000 0.00 0.00 0.00 3.41
2282 2376 5.409826 GGGATTACAGTTCAGTTCAGTTCAG 59.590 44.000 0.00 0.00 0.00 3.02
2283 2377 5.071788 AGGGATTACAGTTCAGTTCAGTTCA 59.928 40.000 0.00 0.00 0.00 3.18
2284 2378 5.552178 AGGGATTACAGTTCAGTTCAGTTC 58.448 41.667 0.00 0.00 0.00 3.01
2294 2388 3.934068 TGAAACGGAGGGATTACAGTTC 58.066 45.455 0.00 0.00 0.00 3.01
2349 2443 6.797454 TCCATAATTATTGGCGTGGTTTTAC 58.203 36.000 0.00 0.00 34.06 2.01
2392 2486 4.049186 CGACACTTATTATGGGACGAAGG 58.951 47.826 0.00 0.00 0.00 3.46
2395 2489 2.691526 AGCGACACTTATTATGGGACGA 59.308 45.455 7.63 0.00 0.00 4.20
2443 2537 8.445275 TGCCATGTGTAACCTAAGTTATTATG 57.555 34.615 0.00 0.00 40.50 1.90
2471 2565 2.449137 AGCCAATAGCCAAGCTTCAT 57.551 45.000 0.00 0.00 45.47 2.57


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.